Evolution of conformational changes in the dynamics of small biological molecules: a hybrid MD/RRK approach

Conformational transitions of glycine induced by vibrational excitation of the O-H stretch

Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the ν=1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (ν=1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.

An exact formulation of hyperdynamics simulations

We introduce a new formula for the acceleration weight factor in the hyperdynamics simulation method, the use of which correctly provides an exact simulation of the true dynamics of a system. This new form of hyperdynamics is valid and applicable where the transition state theory (TST) is applicable and also where the TST is not applicable. To illustrate this new formulation, we perform hyperdynamics simulations for four systems ranging from one degree of freedom to 591 degrees of freedom: (1) We first analyze free diffusion having one degree of freedom. This system does not have a transition state. The TST and the original form of hyperdynamics are not applicable. Using the new form of hyperdynamics, we compute mean square displacement for a range of time. The results obtained agree perfectly with the analytical formula. (2) Then we examine the classical Kramers escape rate problem. The rate computed is in perfect agreement with the Kramers formula over a broad range of temperature. (3) We also study another classical problem: Computing the rate of effusion out of a cubic box through a tiny hole. This problem does not involve an energy barrier. Thus, the original form of hyperdynamics excludes the possibility of using a nonzero bias and is inappropriate. However, with the new weight factor formula, our new form of hyperdynamics can be easily implemented and it produces the exact results. (4) To illustrate applicability to systems of many degrees of freedom, we analyze diffusion of an atom adsorbed on the (001) surface of an fcc crystal. The system is modeled by an atom on top of a slab of six atomic layers. Each layer has 49 atoms. With the bottom two layers of atoms fixed, this system has 591 degrees of freedom. With very modest computing effort, we are able to characterize its diffusion pathways in the exchange-with-the-substrate and hop-over-the-bridge mechanisms.